Package: rmRNAseq
Type: Package
Title: RNA-Seq Analysis for Repeated-Measures Data
Version: 0.1.0
Authors@R: c(person("Yet", "Nguyen", email = "tienyettoan@gmail.com", role = c("aut", "cre")),
    person("Dan", "Nettleton",  role = "aut"), 
    person(c("Charity", "Gordon"), c("Law", "Smyth"), role = "ctb", 
    comment = "The authors of limma::voom, which was modified slightly leading to my_voom"),
    person("Agata", "Michna", role = "ctb", 
    comment = "The author of splineTimeR::splineDiffExprs, which was modified slightly leading to my_splineDiffExprs")
    )
Description: A differential expression analysis method for RNA-seq data from repeated-measures design 
    using general linear model framework and parametric bootstrap inference. The method accounts for 
    the dependence of gene expression levels due to the repeated-measures through continuous autoregressive 
    correlation structure. The method is described in Chapter 4 of 
    Nguyen (2018) <https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=7433&context=etd>.  
Depends: R (>= 3.3)
biocViews:
Imports: AUC (>= 0.3.0), Biobase, DESeq2, edgeR (>= 3.16.5), graphics,
        limma (>= 3.30.13), MASS (>= 7.3-45), Matrix (>= 1.2-8),
        methods, nlme (>= 3.1-131), parallel, reshape (>= 0.8.6),
        rlang, splines, splineTimeR, statmod (>= 1.4.29), stats
License: GPL (>= 2)
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-11-06 16:52:06 UTC; Yet
Author: Yet Nguyen [aut, cre],
  Dan Nettleton [aut],
  Charity Gordon Law Smyth [ctb] (The authors of limma::voom, which was
    modified slightly leading to my_voom),
  Agata Michna [ctb] (The author of splineTimeR::splineDiffExprs, which
    was modified slightly leading to my_splineDiffExprs)
Maintainer: Yet Nguyen <tienyettoan@gmail.com>
Repository: CRAN
Date/Publication: 2019-11-08 13:10:02 UTC
Built: R 3.6.3; ; 2020-08-05 05:04:55 UTC; windows
